The difference is that Real D 3D makes use of the newer and better technology known as circular polarization which offers a better clarity as well as contrast or distinction with a lesser amount of blurriness. IMAX 3D makes use of the linear polarization which does help as much to enhance clarity of vision.
Real-D 3D is a digital stereoscopic projection technology. It is currently the most widely used technology for watching 3D films in theaters. Because Real-D 3D uses a single projector, it suffers a brightness disadvantage. The system causes "significant light loss".
IMAX (an abbreviation for Image Maximum) on the other hand; IMAX-3D has the capacity to record and display images of far greater size and resolution than conventional film systems. To create the illusion of depth, uses separate camera lenses to represent the left and right eyes. This translates a better viewing experience as the screens of IMAX fills your entire field-of-vision (FOV).
In conclusion, Real-D 3D while widely available, sound and image may not always be in sync in quality. Theaters presenting this format are given liberty to customize its systems (ie: Dolby 3D, Dolby 7.1, THX, Screen size, angle of seats, etc..) Meanwhile its rival, IMAX delivers a consistent viewing experience as it requires its theaters all over the world to maintain its strict standards despite its limited locations. Choosing what format to watch really boils down: where are you from? Is there an IMAX theater nearby?